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2018 03 apan

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My presentation at APAN 45 in the joint session with agGateway

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2018 03 apan

  1. 1. eROSA has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 730988 goFAIR The Agrisemantics Project Johannes Keizer, GODAN Secretariat, eROSA project
  2. 2. Horizon 2020 research and innovation programme - grant agreement No 730988 Johannes Keizer APAN 45, 2018-03-28
  3. 3. ......but there are nitty gritty problems Compound Species Concentration (mg/l) Mortality (%) Observations Diazinon Danio rerio 20 10 Diazinon Danio rerio 40 40 Mortality occurs within 30 minutes Example: Research on fish toxicity of Pesticides Active Ingredient Species Concentration (ppm) Dead fish (%) Remarks 二嗪磷 Zebrafish 10 5 二嗪磷 Zebrafish 30 40 Mortality occurs within 30 minutes Lab 1 Lab 2
  4. 4. Horizon 2020 research and innovation programme - grant agreement No 730988 Johannes Keizer APAN 45, 2018-03-28 How to resolve Unifying data schemes and back ends Single data processing for any front end with mapping
  5. 5. Horizon 2020 research and innovation programme - grant agreement No 730988 Johannes Keizer APAN 45, 2018-03-28 Unifying data schemes and back ends ....for ever lasting discussions
  6. 6. Mapping at the front end level DB1 DB2 DB3 DB4
  7. 7. The solution https://www.go-fair.org/
  8. 8. The FAIR principles
  9. 9. An Architecture based on FAIR data Multiple Frontends - Galaxy - R - Portals - D4Science - Excel - PDF - CMS Whatever people want to do Multiple Backends • SQL • Dataverse • CKAN • Text Whatever people want to do Temporary and permanent triple stores Shared Semantics Agroportal - GACS- Maps of Standards - RING APIs to link to all kind of backends APIs to link to all kind of front ends
  10. 10. What we need • Extensive and powerful shared semantics • Performant and scalable triple stores • An API factory that produces APIs which link to any back end and any front end • A powerful dataset/information source discover/registration mechanism
  11. 11. ......solution to the problem Compound (1) Species (1) Concentration (mg/l) (1) Mortality (%) (1) Observations (1) Diazinon (3) Danio rerio (3) 20 10 Diazinon Danio rerio 40 40 Mortality occurs within 30 minutes Example: Research on fish toxicity of Pesticides Lab 1 1) http://agroportal.lirmm.fr/ontologies/toxtestont 2) http://browser.agrisemantics.org/gacs/en/page/C15291 3) http://browser.agrisemantics.org/gacs/en/page/C9983 http://bioportal.bioontology.org/ontologies/NCBITAXON?p=classes&conceptid= 7955
  12. 12. http://browser.agrisemantics.org/gacs /en/page/C15291
  13. 13. ......the problem is resolvable Compound Species Concentration (mg/l) Mortality (%) Observations Diazinon Danio rerio 20 10 Diazinon Danio rerio 40 40 Mortality occurs within 30 minutes Example: Research on fish toxicity of Pesticides Active Ingredient Species Concentration (ppm) Dead fish (%) Remarks 二嗪磷 Zebrafish 10 5 二嗪磷 Zebrafish 30 40 Mortality occurs within 30 minutes Lab 1 Lab 2
  14. 14. A global attempt
  15. 15. Metada passport from fairshairing
  16. 16. Our contribution http://agrisemantics.org/
  17. 17. GACS http://browser.agrisemantics.org/gacs/en/
  18. 18. Agroportal http://agroportal.lirmm.fr/
  19. 19. The CIARD RING
  20. 20. A record from the RING
  21. 21. Horizon 2020 research and innovation programme - grant agreement No 730988 Johannes Keizer APAN 45, 2018-03-28 What is the GACS? Global Agricultural Concept Space Stable URIs with as little semantic determination as possible Interoperability Switchboard Reusable concepts Mapping on low level
  22. 22. GACS – born from merging 3 thesauri
  23. 23. service 2 GACS Thes etc. thes1 Onto1 Onto2 Onto3 Onto An interoperability Switchboard Yes, very much oversimplified, but....
  24. 24. Horizon 2020 research and innovation programme - grant agreement No 730988 Johannes Keizer APAN 45, 2018-03-28 A vision of the process A community needs a new Ontology/Taxonomy/Thesaurus/........... It consults GACS vocabularies for an informed decison It constructs it’s own KOS It checks, where classes/concept/terms have a related instance in GACS If yes, it creates the appropriate semantic relationship If no, it evaluates if the new concept is of common interest If yes, it adds the concept to GACS
  25. 25. But..... The existing GACS module is already able to crosslink different KOS, link your concepts and classes to GACS concepts add your URIs to GACS
  26. 26. AgroPortal an ontology repository for agronomy, food, plant sciences & biodiversity Publish, search, download Browse, visualize Peer review Versioning Annotation Recommendati on Mapping Notes Projects 77 ontologies, 95 candidates 5 driving use cases ~90 registered users http://agroportal. lirmm.fr
  27. 27. Conclusion: state of Infrastructure

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